GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

RR42_RS28305, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

Rules

Overview: L-threonine degradation in GapMind is based on MetaCyc pathway I via 2-ketobutyrate formate-lyase (link), pathway II via glycine (link), pathway III via methylglyoxal (link), and pathway IV via threonine aldolase (link). Pathway V is not thought to occur in prokaryotes and is not included.

70 steps (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
RR42_RS28305 L-threonine:H+ symporter AU252_RS15260 AU252_RS08100
ltaE L-threonine aldolase AU252_RS02110 AU252_RS09420
adh acetaldehyde dehydrogenase (not acylating) AU252_RS16200 AU252_RS12650
ackA acetate kinase AU252_RS15110
pta phosphate acetyltransferase AU252_RS15080
gcvP glycine cleavage system, P component (glycine decarboxylase) AU252_RS15225 AU252_RS06310
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) AU252_RS15230 AU252_RS09435
gcvH glycine cleavage system, H component (lipoyl protein) AU252_RS02660 AU252_RS15235
lpd dihydrolipoyl dehydrogenase AU252_RS02335 AU252_RS03920
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AU252_RS02190
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AU252_RS02190
acs acetyl-CoA synthetase, AMP-forming AU252_RS14440 AU252_RS07515
ald-dh-CoA acetaldehyde dehydrogenase, acylating AU252_RS17310
aldA lactaldehyde dehydrogenase AU252_RS14785 AU252_RS01555
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AU252_RS04345
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AU252_RS04325 AU252_RS00670
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AU252_RS04330 AU252_RS00900
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AU252_RS04335 AU252_RS00660
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AU252_RS04340 AU252_RS00890
D-LDH D-lactate dehydrogenase AU252_RS06485 AU252_RS16225
dddA 3-hydroxypropionate dehydrogenase AU252_RS07805
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) AU252_RS06485
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) AU252_RS06485
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) AU252_RS12890 AU252_RS20705
grdA glycine reductase component A1
grdB glycine reductase component B, gamma subunit
grdC glycine reductase component C, beta subunit
grdD glycine reductase component C, alpha subunit
grdE glycine reductase component B, precursor to alpha/beta subunits
hpcD 3-hydroxypropionyl-CoA dehydratase AU252_RS07800 AU252_RS00745
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AU252_RS07815 AU252_RS22410
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) AU252_RS03690 AU252_RS00620
L-LDH L-lactate dehydrogenase AU252_RS14590
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component AU252_RS06485
lctO L-lactate oxidase or 2-monooxygenase AU252_RS14590
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit
lutB L-lactate dehydrogenase, LutB subunit
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit AU252_RS03875 AU252_RS09860
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AU252_RS03875 AU252_RS01380
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit AU252_RS03425
pccB propionyl-CoA carboxylase, beta subunit AU252_RS03835 AU252_RS03430
pco propanyl-CoA oxidase AU252_RS21750 AU252_RS03530
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase AU252_RS00960 AU252_RS07200
prpC 2-methylcitrate synthase AU252_RS02765 AU252_RS17710
prpD 2-methylcitrate dehydratase AU252_RS02755
prpF methylaconitate isomerase
serP1 L-threonine uptake transporter SerP1 AU252_RS15260 AU252_RS08100
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase AU252_RS04295 AU252_RS13625
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase AU252_RS03695 AU252_RS01730
tynA aminoacetone oxidase AU252_RS12820 AU252_RS24560 with AU252_RS24565
yvgN methylglyoxal reductase (NADPH-dependent) AU252_RS06040 AU252_RS21070

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory